Introduction to Sockeye

Tony Liang

University of British Columbia

Land acknowledgement

I would like to acknowledge that I work on the traditional, ancestral, and unceded territory of the Coast Salish Peoples, including the territories of the xwməθkwəy̓əm (Musqueam), Skwxwú7mesh (Squamish), Stó:lō and Səl̓ílwətaʔ/Selilwitulh (Tsleil- Waututh) Nations.

Traditional: Traditionally used and/or occupied by Musqueam people

Ancestral: Recognizes land that is handed down from generation to generation

Unceded: Refers to land that was not turned over to the Crown (government) by a treaty or other agreement

Setup VSCode

Checkout the instruction of your right platform below:

Open this link to download, once it is finished:

  1. Open the downloaded VSCode-darwin-universal.zip file
  2. Move the extracted VS Code app from Downloads to Applications (Located to your left under Favorites)
  3. Launch VS Code and open the Command Palette by Cmd + Shift + P
  4. Type shell command
  5. Select the option: Install code command in PATH
  6. Restart your terminal and try entering: code --version to confirm successful installation

Open this link to download.

Run the installer, accept default config except:

  • On Select Additional Tasks
    • Add ‘Open with Code action to Windows file context menu’
    • Add ‘Open with Code’ action to Windows directory context menu”
    • Register Code as an editor for supported file types
    • Add to PATH (should be selected by default)

Connecting to Sockeye

Note

You need to have a UBC IP address in order to access to the server by connecting to eduroam or ubcsecure

Login to sockeye with the ssh command:

ssh cwl@sockeye.arc.ubc.ca

  • cwl is your campus wide login

  • password is your same CWL password

  • sockeye.arc.ubc.ca is the server address

  • you also need Two-Factor Authentication 2FA

Alternative way connecting to Sockeye

Generate a new ssh key pair

ssh-keygen -t rsa
  • Follow the defaults by prompting Enter
  • Passphrase Optional
  • Two keys generated:
    • one public (id_rsa.pub)
    • one private (id_rsa)

Caution

Keep the private key safe and for your use only

Add your public key to the server

# Need to replace cwl!
ssh-copy-id -i ~/.ssh/id_rsa.pub
# Need to replace cwl!
type $env:USERPROFILE\.ssh\id_rsa.pub | ssh cwl@sockeye.arc.ubc.ca "cat >> .ssh/authorized_keys"

Use any editor to create ~/.ssh/config and enter the following:

# Note these indent matters
Host  arc # or another alias you like
  HostName sockeye.arc.ubc.ca
  User cwl # replace your cwl

  • Host = User@Hostname

  • Multiple configuration (multiple servers)

  • More options available , look at here

Sockeye

Sockeye is a “high performance computing” (HPC) platform

  • Use it to run large computational works
  • Upon login, you’re on a “login” node
  • You can log out and leave a job running
  • Runs with PBS, changing to SLURM soon

Another Slide here

New slide, should have a pause

Show later

Terminal

This is left column

This is right column

Yet another slide with tabsets

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